[gmx-users] nucleic acis simulation

[David van der Spoel]

Miguel Ortiz Lombardia wrote:
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> David van der Spoel escribió el 28/02/06 11:25 :
>> Miguel Ortiz Lombardia wrote:
>> Thank you Maik.
>>
>> The AMBER ports are some I'm testing, sure.
>> BTW, I can't get it ready if I solvate the model. Everything goes fine
>> until grompp complains:
>>
>> $> grompp -v -f em -c watered -o em -p nucT
>>
>> (...)
>>
>> -------------------------------------------------------
>> Program grompp, VERSION 3.3
>> Source code file: toppush.c, line: 1108
>>
>> Fatal error:
>> [ file "/usr/local/gromacs/share/gromacs/top/spc.itp", line 41 ]:
>>              Atom index (1) in settles out of bounds (1-0)
>> -------------------------------------------------------
>>
>> Any clues of what may be wrong?
>>
>>> order of bits in the topology file. chpater 5
> 
> The order of the elements in the topology file seem the same whether
> this is created using ffG43a1 or ffamber99. However, only the second
> prompts the error at the grompp step. I read the topology and
> molecule.itp file formats in chapter 5 of the manual (v. 3.2), but I was
> not able to spot the problem. Could you please be more precise?
> 
> Thank you!
> 
> 
> Miguel
> - --
> Miguel Ortiz Lombardía
> Centro de Investigaciones Oncológicas
> C/ Melchor Fernández Almagro, 3
> 28029 Madrid, Spain
> Tel. +34 912 246 900
> Fax. +34 912 246 976
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> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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> Dans les jardins mal fréquentés!
>                                                        Georges Brassens
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the position in the top file where the spc.itp was included is wrong.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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